scholarly journals Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Piroon Jenjaroenpun ◽  
Visanu Wanchai ◽  
Kikumi D. Ono-Moore ◽  
Jennifer Laudadio ◽  
Laura P. James ◽  
...  

ABSTRACT Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
César G. Albariño ◽  
Lisa Wiggleton Guerrero ◽  
Ayan K. Chakrabarti ◽  
Pierre E. Rollin ◽  
Stuart T. Nichol

Monongahela hantavirus was first identified in deer mice and was later found responsible for hantavirus pulmonary syndrome cases in Pennsylvania and West Virginia in the United States. Here, we report the complete sequences of Monongahela virus S, M, and L genomic segments obtained from a fatal clinical case reported in 1997.


2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Richard C. White ◽  
Manolito Torralba ◽  
Kelly Colt ◽  
Frank Harrison ◽  
Karrie Goglin ◽  
...  

Neisseria gonorrhoeae is the etiological agent of gonorrhea, the second most common notifiable disease in the United States. Here, we used a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequencing data to obtain closed genome sequences of nine clinical N. gonorrhoeae isolates.


2021 ◽  
Author(s):  
Elijah Kolawole Oladipo ◽  
Boluwatife Ayobami Irewolede ◽  
Precious Moyosoluwa Oyewole ◽  
Emmanuel Oluwatobi Dairo ◽  
Ayodele Eugene Ayeni ◽  
...  

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Understanding the transmission dynamics of SARS-CoV-2 contamination in the environment is essential for infection control policies. This study aims to provide a phylodynamic analysis and distribution pattern of SARS-CoV-2 from the environment in terms of Source, clades, lineages, and their location. Ninety (90) retrieved whole-genome sequences of environmental sources from GISAID were investigated to determine the evolutionary process of SARS-CoV-2 and mutation in the isolated nucleotide sequences. The analysis was carried out using R, MAFFT, and MEGA X software. Out of the five countries studied, Austria has the highest distribution with sixty-five samples (72.2%), and the highest isolates of 68 (75.6%) were from raw sewage. The highest clade in circulation as obtained from the study is G with lineages B. The phylogeny of SARS-CoV-2 whole-genome sequences from Austria, the United States, China, Brazil, and Liechtenstein indicated that the SARS-CoV-2 viruses were all clustered together, irrespective of sequence geographic location. The study concluded by demonstrating a clear interconnection between the phylogeny of SARS-CoV-2 isolates from various geographic locations, all of which were locked in the same cluster regardless of their environment specimen. Thus, depicting the possibility of their origination from a common ancestor.


2021 ◽  
Vol 17 (6) ◽  
pp. e1009619
Author(s):  
Yosuke Hirotsu ◽  
Masao Omata

We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad. After identifying these cases, we developed a TaqMan assay to screen for the above hallmark mutations and identified an additional 14 patients with the same mutations. The associated virus strain was classified into the GR clade (Global Initiative on Sharing Avian Influenza Data [GISAID]), 20B clade (Nextstrain), and R.1 lineage (Phylogenetic Assignment of Named Global Outbreak [PANGO] Lineages). As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.


Science ◽  
2021 ◽  
Vol 372 (6538) ◽  
pp. eabg3055 ◽  
Author(s):  
Nicholas G. Davies ◽  
Sam Abbott ◽  
Rosanna C. Barnard ◽  
Christopher I. Jarvis ◽  
Adam J. Kucharski ◽  
...  

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in September 2020 and is rapidly spreading toward fixation. Using a variety of statistical and dynamic modeling approaches, we estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine rollout, COVID-19 hospitalizations and deaths across England in the first 6 months of 2021 were projected to exceed those in 2020. VOC 202012/01 has spread globally and exhibits a similar transmission increase (59 to 74%) in Denmark, Switzerland, and the United States.


Author(s):  
Yunfan Fan ◽  
Andrew N Gale ◽  
Anna Bailey ◽  
Kali Barnes ◽  
Kiersten Colotti ◽  
...  

Abstract We present a highly contiguous genome and transcriptome of the pathogenic yeast, Candida nivariensis. We sequenced both the DNA and RNA of this species using both the Oxford Nanopore Technologies (ONT) and Illumina platforms. We assembled the genome into an 11.8 Mb draft composed of 16 contigs with an N50 of 886 Kb, including a circular mitochondrial sequence of 28 Kb. Using direct RNA nanopore sequencing and Illumina cDNA sequencing, we constructed an annotation of our new assembly, supplemented by lifting over genes from Saccharomyces cerevisiae and Candida glabrata.


2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Yuhuan Qiu ◽  
Zehui Zhao ◽  
Jianming Qiu

We are reporting the sequences of seven complete genomes of parvovirus B19, which were extracted from human plasma specimens collected in the United States. The seven B19 genome sequences, which are 5,596 nucleotides long and include the inverted terminal repeats (ITRs), share an identity of 96.73%.


2021 ◽  
Vol 12 ◽  
pp. 591
Author(s):  
Russell L. Blaylock

The ongoing “pandemic” involving the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) has several characteristics that make it unique in the history of pandemics. This entails not only the draconian measures that some countries and individual states within the United States and initiated and made policy, most of which are without precedent or scientific support, but also the completely unscientific way the infection has been handled. For the 1st time in medical history, major experts in virology, epidemiology, infectious diseases, and vaccinology have not only been ignored, but are also demonized, marginalized and in some instances, become the victim of legal measures that can only be characterized as totalitarian. Discussions involving various scientific opinions have been eliminated, top scientists have been frightened into silence by threats to their careers, physicians have lost their licenses, and the concept of early treatment has been virtually eliminated. Hundreds of thousands of people have died needlessly as a result of, in my opinion and the opinion of others, poorly designed treatment protocols, mostly stemming from the Center for Disease Control and Prevention, which have been rigidly enforced among all hospitals. The economic, psychological, and institutional damage caused by these unscientific policies is virtually unmeasurable. Whole generations of young people will suffer irreparable damage, both physical and psychological, possibly forever. The truth must be told.


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